rs6938674

Variant names:

• chr6-31440227-T-C
• rs6938674
• ENST00000673857.1:n.63-22896T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000673857.1(ENSG00000288587):​n.63-22896T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0334 in 151,922 control chromosomes in the GnomAD database, including 142 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.033 (142 hom., cov: 31)
• Consequence: ENSG00000288587 ENST00000673857.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.237

Genes affected

ENSG00000288587 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0739 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288587	ENST00000673857.1	n.63-22896T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0333 AC: 5059 AN: 151804 Hom.: 137 Cov.: 31

Gnomad AFR AF: 0.0302

Gnomad AMI AF: 0.00549

Gnomad AMR AF: 0.0280

Gnomad ASJ AF: 0.0338

Gnomad EAS AF: 0.0801

Gnomad SAS AF: 0.0264

Gnomad FIN AF: 0.0231

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0351

Gnomad OTH AF: 0.0398

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0334 AC: 5079 AN: 151922 Hom.: 142 Cov.: 31 AF XY: 0.0332 AC XY: 2467 AN XY: 74294

Gnomad4 AFR AF: 0.0303

Gnomad4 AMR AF: 0.0280

Gnomad4 ASJ AF: 0.0338

Gnomad4 EAS AF: 0.0803

Gnomad4 SAS AF: 0.0266

Gnomad4 FIN AF: 0.0231

Gnomad4 NFE AF: 0.0351

Gnomad4 OTH AF: 0.0465

Alfa AF: 0.0347 Hom.: 113

Bravo AF: 0.0331

Asia WGS AF: 0.0510 AC: 178 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.2
DANN	Benign	0.77

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs6938674; hg19: chr6-31408004;